Merge branch 'main' of https://github.com/xieguigang/mzkit_docs

xieguigang · Feb 6, 2024 · 25a76d7 · 25a76d7
2 parents 5a9ea5a + eb82cd9
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diff --git a/assets/js/R_syntax.d.ts b/assets/js/R_syntax.d.ts
@@ -1,5 +1,8 @@
 declare namespace Token {
     type tokenType = "undefined" | "number" | "character" | "logical" | "factor" | "keyword" | "symbol" | "operator" | "comment" | "newLine" | "whitespace" | "bracket" | "terminator" | "color" | "delimiter";
+    /**
+     * regexp for test html colors
+    */
     const html_color: RegExp;
     /**
      * pattern for match the number token
@@ -14,6 +17,7 @@ declare namespace Token {
     const operators: {};
     const stacks: {};
     const keywords: {};
+    function isColorLiteral(pull_str: string): boolean;
 }
 declare class TokenParser {
     source: string;
@@ -34,7 +38,7 @@ declare class TokenParser {
     private walkChar;
     private measureToken;
 }
-declare type token = Token.token;
+type token = Token.token;
 declare function parseText(str: string): token[];
 /**
  * parse the script text to syntax highlight html content

diff --git a/assets/js/R_syntax.js b/assets/js/R_syntax.js
diff --git a/assets/js/R_syntax.js.map b/assets/js/R_syntax.js.map
diff --git a/docs/install-on-linux.md b/docs/install-on-linux.md
@@ -0,0 +1,38 @@
+# 在Linux系统上安装MZKit桌面工作站
+
+<!-- 2024-01-22 -->
+
+```bash
+dnf -y update
+reboot
+dnf groupinstall 'Development Tools' -y
+dnf -y install epel-release
+dnf config-manager --set-enabled powertools
+dnf -y install libxslt-devel libpng-devel libX11-devel zlib-devel libtiff-devel freetype-devel libxcb-devel  libxml2-devel libgcrypt-devel dbus-devel libjpeg-turbo-devel  fontconfig-devel gnutls-devel gstreamer1-devel libXcursor-devel libXi-devel libXrandr-devel libXfixes-devel libXinerama-devel libXcomposite-devel mesa-libOSMesa-devel libpcap-devel libusb-devel libv4l-devel libgphoto2-devel gstreamer1-devel libgudev SDL2-devel gsm-devel libvkd3d-devel libudev-devel make cmake gcc flex
+```
+
+```bash
+wget https://dl.winehq.org/wine/source/9.0/wine-9.0.tar.xz
+tar xvf wine-9.0.tar.xz
+cd wine-*/
+./configure --enable-win64 
+make
+sudo make install
+```
+
+```bash
+wine64 --version
+wine --help
+```
+
+
+```bash
+sudo dnf install wine-core
+sudo dnf install yum-utils
+
+sudo dnf config-manager --set-enabled crb
+sudo dnf install epel-release
+sudo dnf install epel-next-release
+
+sudo dnf install mesa-libOSMesa
+```
diff --git a/vignettes/MSImaging/MSImaging/MSIfilter.html b/vignettes/MSImaging/MSImaging/MSIfilter.html
@@ -82,6 +82,12 @@ <h1>MSIfilter</h1>
       <table class="table-three-line">
         <caption>.NET clr function exports</caption>
         <tbody><tr>
+  <td id="intensity_cut">
+    <a href="./MSIfilter/intensity_cut.html">intensity_cut</a>
+  </td>
+  <td><p>removes low intensity spots</p></td>
+</tr>
+<tr>
   <td id="log_scale">
     <a href="./MSIfilter/log_scale.html">log_scale</a>
   </td>

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/TrIQ_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/TrIQ_scale.html
@@ -45,9 +45,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/denoise_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/denoise_scale.html
@@ -42,9 +42,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: none">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/intensity_cut.html b/vignettes/MSImaging/MSImaging/MSIfilter/intensity_cut.html
@@ -0,0 +1,76 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>removes low intensity spots</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>intensity_cut {MSIfilter}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>removes low intensity spots</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>intensity_cut</strong>(
+    <i>threshold</i> = <span style='color: green;'>0.05</span>,
+    <i>quantile</i> = <span style='color: blue !important;'>FALSE</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>threshold</dt>
+<dd><p><p>-</p></p></dd>
+
+
+<dt>quantile</dt>
+<dd><p><p>-</p></p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        BioNovoGene
+
+        <h3>Value</h3>
+
+        this function returns data object of type <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/IntensityCutScaler.html">IntensityCutScaler</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/IntensityCutScaler.html">IntensityCutScaler</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>MSIfilter</em> version 1.0.0.0 <a
+                href="../MSIfilter.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("example_r");</script>
+
+</html>
diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/knn_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/knn_scale.html
@@ -50,9 +50,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/log_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/log_scale.html
@@ -45,9 +45,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/quantile_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/quantile_scale.html
@@ -42,9 +42,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: none">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/MSIfilter/soften_scale.html b/vignettes/MSImaging/MSImaging/MSIfilter/soften_scale.html
@@ -41,9 +41,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot.html b/vignettes/MSImaging/MSImaging/ggplot.html
@@ -121,7 +121,7 @@ <h1>ggplot</h1>
   <td id="raster_blending">
     <a href="./ggplot/raster_blending.html">raster_blending</a>
   </td>
-  <td></td>
+  <td><p>rendering a gdi+ heatmap for create raster annotation in ggplot layer</p></td>
 </tr>
 <tr>
   <td id="geom_msimaging">

diff --git a/vignettes/MSImaging/MSImaging/ggplot/MSI_dimension.html b/vignettes/MSImaging/MSImaging/ggplot/MSI_dimension.html
@@ -48,9 +48,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot/MSI_gaussblur.html b/vignettes/MSImaging/MSImaging/ggplot/MSI_gaussblur.html
@@ -45,9 +45,9 @@ <h3 style="display: block;">Details</h3>
 
         <p>the gauss blur function is not working well on the linux platform</p>
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>
 

diff --git a/vignettes/MSImaging/MSImaging/ggplot/MSI_knnfill.html b/vignettes/MSImaging/MSImaging/ggplot/MSI_knnfill.html
@@ -53,9 +53,9 @@ <h3 style="display: none;">Details</h3>
 
 
 
-        <h3 style="display: bloc">Authors</h3>
+        <h3 style="display: block">Authors</h3>
 
-
+        BioNovoGene
 
         <h3>Value</h3>